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Revision 730

Added by Aaron Marcuse-Kubitza almost 13 years ago

join: Report which input mappings are missing a mapping in the join map

View differences:

inputs/SALVIAS/maps/VegBIEN.organisms.csv
38 38 
PlotCode,,"Brad: Same as plotCode, above"
39 39 
SourceVoucher,,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
40 40 
SpAuthStatus,,
41 
canopy_form,,Brad: Should also be userDefined for VegBank.
42 
canopy_position,,Brad: Should also be userDefined for VegBank.
41 
canopy_form,,** No join mapping for /simpleUserdefined[name=canopyForm]/value ** Brad: Should also be userDefined for VegBank.
42 
canopy_position,,** No join mapping for /simpleUserdefined[name=canopyPosition]/value ** Brad: Should also be userDefined for VegBank.
43 43 
coll_inits,,
44 44 
collector_code,,Brad: OMIT
45 45 
common_name,,
......
51 51 
height_m_commercial,,
52 52 
ind_id,,Brad: OMIT
53 53 
infra_auth_1,,
54 
liana_infestation,,Brad: Should also be userDefined for VegBank.
54 
liana_infestation,,** No join mapping for /simpleUserdefined[name=lianaInfestation]/value ** Brad: Should also be userDefined for VegBank.
55 55 
morphocf,,
56 56 
morphoname,,
57 57 
name_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."
bin/join
16 16 
    reader = csv.reader(stream)
17 17 
    map_1_in, map_1_out = reader.next()[:2]
18 18 
    for row in reader:
19 
        if row[1] != '': map_1[row[0]] = row[1]
19 
        if row[0] != '': map_1[row[0]] = row[1]
20 20 
    stream.close()
21 21
22 22 
    # Join map 1 to map 0
......
28 28 
    cols[1] = map_1_out
29 29 
    writer.writerow(cols)
30 30 
    for row in reader:
31 
        row[1] = map_1.get(row[1], '')
31 
        if row[1] != '':
32 
            try: row[1] = map_1[row[1]]
33 
            except KeyError:
34 
                row[2] = '** No join mapping for '+row[1]+' ** '+row[2]
35 
                row[1] = ''
32 36 
        writer.writerow(row)
33 37 

  		




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main()


  		












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